Ok I found what took so long.
First the reset file permissions, when you did the other drives besides C:\ you have a LOT of folders, so those took some time.
But the part that I found the strangest is the one repair that took over 2 hours! And it was just deleting temp files!
13 - Remove Temp Files
Start (19.1.2014 05:27:35)
Running Repair Under System Account
Done (19.1.2014 07:33:30)
The delete temp files is a very easy and fast repair. It is one line of code that uses the built in delete command for all files under the temp folder. No way it should have taken two hours, UNLESS something was continuing to add files back into the temp folder. Viruses will do this a lot, when you delete one part of it another part recreates it.
So the repair was deleting files while something kept adding them back, and thus how a normally 10 sec repair took over 2 hours.
So I think the best thing to do is to run some scans first.
Have you run malwarebytes anti root kit tool or combofix.exe yet?
Shane